Saturday, June 28, 2008

Research News

Links to some Science Daily articles follow. They cover a range of topics with some news on each one.

Cell Surface Receptors Are All 'Talk' In T Cell Stimulation

This article explores immunological cells known as T cells which contain proteins on the surfaces of their cells known as antigens and integrins. Integrins enable T cells to latch onto things. Discovering how coordinated function occurs between the different cell surface receptors was a goal of researchers.

Key Regulator Of DNA Mutations Identified

Mutations are generally thought of as changes in DNA that are random with respect to fitness. However, as the above article points out, some mutations within immunological cells known as B lymphocytes, are induced. A protein known as AID changes a segment of DNA which encodes antibodies. The induced change can enable an antibody to bind to a different target or can enable a tighter cling to an already existing target. A type of RNA called miR-155 is able to bind to AID and regulate it and the mutation process it fosters.

Key Step In Programmed Cell Death Discovered

Apoptosis, commonly characterized as programmed cell death, is a mechanism enabling eukaryotic organisms to rid themselves of defective cells. But like any process the mechanisms enabling apoptosis can break down. To be effective apoptosis must be correctly regulated. Too much control may mean that defective cells are not killed off and too little may mean that healthy cells are killed.

The linked article notes that St. Jude Children's Research Hospital researchers have identified proteins which restrain apoptosis. If a full complement of needed proteins is not present then the ability to restrain apoptosis can be compromised. Results were published in the journal Nature.

Infectious And Non-infectious Prions Have Clear Differences In Molecular Structures

Infectious and non-infectious prions are differently structured at differing pH levels. The infectious version (pH 7) was described as having both rigid domains and highly flexible loops.


Monday, June 16, 2008

Nucleotide Excision Repair

BioSolutions has an entry about the nucleotide excision repair pathway which also features an animation. Quoting from the blog:

Nucleotide excision repair is a DNA repair mechanism. DNA constantly requires repair due to damage that can occur to bases from a vast variety of sources including chemicals but also ultraviolet (UV) light from the sun. Nucleotide excision repair (NER) is a particularly important mechanism by which the cell can prevent unwanted mutations by removing the vast majority of UV-induced DNA damage (mostly in the form of thymine dimers and 6-4-photoproducts). The importance of this repair mechanism is evidenced by the severe human diseases that result from in-born genetic mutations of NER proteins including Xeroderma pigmentosum and Cockayne's syndrome. While the base excision repair machinery can recognize specific lesions in the DNA and can correct only damaged bases that can be removed by a specific glycosylase, the nucleotide excision repair enzymes recognize bulky distortions in the shape of the DNA double helix. Recognition of these distortions leads to the removal of a short single-stranded DNA segment that includes the lesion, creating a single-strand gap in the DNA, which is subsequently filled in by DNA polymerase, which uses the undamaged strand as a template. NER can be divided into two subpathways (Global genomic NER and Transcription coupled NER) that differ only in their recognition of helix-distorting DNA damage.

Maintaining genomic integrity is essential for living organisms. NER is a major pathway allowing the removal of lesions which would otherwise accumulate and endanger the health of the affected organism. BioSolutions is a great site for those with an interest in biology.


Thursday, June 12, 2008

Design Inteligente: An ID Blog in Portuguese

Design Inteligente is one of the better ID blogs which has recently come to my attention. Paulo J. is the author. His blog is artfully illustrated and has a pleasing appearance. It also has substance. The primary language of the blog is Portuguese but it contains flags representing different languages which one can click on and get a translation. Let's look at one blog entry in particular which is titled O que é o Design Inteligente? which means What is Intelligent Design? That's as basic as it gets.

The blog entry links to an article by William Dembski and uses the game of scrabble to make a point about how intelligent input is recognizable. Outcomes, attributed to natural causes directed by an intelligent agency, can do what undirected natural causes cannot- place scrabble letters in meaningful sequential order. There is a clear parallel to biology. DNA is functional because its codon symbols have symbolic significance. They enable the synthesis of biologically functional proteins. The source of these molecular symbols is not explained by an evolutionary process which presumes the existence of a replicating cell. Functional cells come already loaded with meaningful order of nucleotides within codons as well as a system enabling the translation of these symbols. The sequencing of symbols, be it scrabble letters or nucleotide "letters," allows us to distinguish directed natural causes from undirected natural causes.

At the end of the blog entry appears this quote of a familiar person:

The generation of information stored and transported within systems is a symbolic indicator of design. Alphanumeric symbols have their counterparts in the field of biology - codons composed of "letters" in the form of nucleotides.

- William Bradford

Wednesday, June 04, 2008

Turning the Tables

Dr. Michael Egnor posted The Hard and Easy Problems in the Mind-Brain Question at Evolution News and Views. Egnor has this to say:

The hard problem of consciousness is the most important problem in understanding the mind, and thus far materialism has provided no insight. It is unclear how it even could provide insight. Nothing about the scientific characterization of matter—and nothing about materialism—explains the emergence of subjective experience. The principal materialist response to this catastrophe for materialist ideology has been to deny the relevance of subjective experience to our understanding of the mind. Yet the retreat to science and the denial of the relevance of philosophy is no refuge. Science is natural philosophy.

Materialists, left with the choice of denying materialism or denying the reality of subjective mental experience, deny subjective mental experience. There is no fanaticism like materialist fanaticism.

Egnor turns a favorite tactic of materialists against them. Materialists like to refer to the material nature of the brain in arguing against duality. But the material nature of the brain demands explanations that are consistent with materialism and Egnor has highlighted the fact that no insight into subjective experiences is forthcoming from a materialist perspective. He who lives by the sword...